| 1. |
- Bolmgren, Kjell, et al.
(författare)
-
One man, 73 years, and 25 species. Evaluating phenological responses using a lifelong study of first flowering dates
- 2013
-
Ingår i: International journal of biometeorology. - : Springer Science and Business Media LLC. - 0020-7128 .- 1432-1254. ; 57:3, s. 367-375
-
Tidskriftsartikel (refereegranskat)abstract
- Phenological shifts linked to global warming reflect the ability of organisms to track changing climatic conditions. However, different organisms track global warming differently and there is an increasing interest in the link between phenological traits and plant abundance and distribution. Long-term data sets are often used to estimate phenological traits to climate change, but so far little has been done to evaluate the quality of these estimates. Here, we use a 73-year long data series of first flowering dates for 25 species from north-temperate Sweden to evaluate (i) correlations between first flowering dates and year for different time periods and (ii) linear regression models between first flowering date and mean monthly temperatures in preceding months. Furthermore, we evaluate the potential of this kind of data to estimate the phenological temperature sensitivities (i.e. number of days phenological change per degree temperature change, beta(60)) in such models. The sign of the correlations between first flowering dates and year were highly inconsistent among different time periods, highlighting that estimates of phenological change are sensitive to the specific time period used. The first flowering dates of all species were correlated with temperature, but with large differences in both the strength of the response and the period(s) of the year that were most strongly associated with phenological variation. Finally, our analyses indicated that legacy data sets need to be relatively long-term to be useful for estimating phenological temperature sensitivities (beta(60)) for inter-specific comparisons. In 10-year long observation series only one out of 24 species reached a parts per thousand yen80 % probability of estimating temperature sensitivity (beta(60)) within a +/- 1 range, and 17 out of 24 species reached a parts per thousand yen80 % probability when observation series were 20 years or shorter. The standard error for beta(60) ranged from 0.6 to 2.0 for 10-year long observation series, and 19 out of 24 species reached SE < 1 after 15 years. In general, late flowering species will require longer time series than early flowering species.
|
|
| 2. |
- Liljenström, Hans
(författare)
-
Multi-scale Causation in Brain Dynamics
- 2016
-
Ingår i: Cognitive Phase Transitions in the Cerebral Cortex - Enhancing the Neuron Doctrine by Modeling Neural Fields. - Cham : Springer International Publishing. - 9783319244044 ; 39:39, s. 177-186
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- For any complex system, consisting of several organizational levels, the problem of causation is profound. Usually, science considers upward causation as funda-mental, paying less or no attention to any downward causation. This is also true for the nervous system, where cortical neurodynamics, or even higher mental functions of the brain are normally considered causally dependent on the nerve cell activity, or even the activity at the ion channel level. This study presents both upward and downward causation in cortical neural systems, using computational methods with focus on cortical fluctuations. We have developed models of paleo- and neocortical structures, in order to study their mesoscopic neurodynamics, as a link between the microscopic neuronal and macroscopic mental events and pro-cesses. We demonstrate how both noise and chaos may play a role for the func-tions of cortical structures. While microscopic random noise may trigger meso- or macroscopic states, the nonlinear dynamics at these levels may also affect the ac-tivity at the microscopic level.
|
|
| 3. |
- Seibert, M. Marvin, et al.
(författare)
-
Single mimivirus particles intercepted and imaged with an X-ray laser
- 2011
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 470:7332, s. 78-81
-
Tidskriftsartikel (refereegranskat)abstract
- X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions(1-4). Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma(1). The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval(2). Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a noncrystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source(5). Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
|
|
| 4. |
|
|
| 5. |
- Abelein, Axel, et al.
(författare)
-
Transient small molecule interactions kinetically modulate amyloid beta peptide self-assembly
- 2012
-
Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 586:22, s. 3991-3995
-
Tidskriftsartikel (refereegranskat)abstract
- Small organic molecules, like Congo red and lacmoid, have been shown to modulate the self-assembly of the amyloid beta peptide (A beta). Here, we show that A beta forms NMR invisible non-toxic co-aggregates together with lacmoid as well as Congo red. We find that the interaction involves two distinct kinetic processes and at every given time point only a small fraction of A beta is in the co-aggregate. These weak transient interactions kinetically redirect the aggregation prone A beta from self-assembling into amyloid fibrils. These findings suggest that even such weak binders might be effective as therapeutics against pathogenic protein aggregation.
|
|
| 6. |
- Agback, Peter, et al.
(författare)
-
H-1, C-13 and N-15 resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution
- 2022
-
Ingår i: Biomolecular Nmr Assignments. - : Springer Science and Business Media LLC. - 1874-2718 .- 1874-270X. ; 16, s. 135-145
-
Tidskriftsartikel (refereegranskat)abstract
- The serotype II Dengue (DENV 2) virus is the most prevalent of all four known serotypes. Herein, we present nearly complete H-1, N-15, and C-13 backbone and H-1, C-13 isoleucine, valine, and leucine methyl resonance assignment of the apo S135A catalytically inactive variant of the DENV 2 protease enzyme folded as a tandem formed between the serine protease domain NS3pro and the cofactor NS2B, as well as the secondary structure prediction of this complex based on the assigned chemical shifts using the TALOS-N software. Our results provide a solid ground for future elucidation of the structure and dynamic of the apo NS3pro/NS2B complex, key for adequate development of inhibitors, and a thorough molecular understanding of their function(s).
|
|
| 7. |
- Dimarogona, Maria, et al.
(författare)
-
Interactions of a fungal lytic polysaccharide monooxygenase with beta-glucan substrates and cellobiose dehydrogenase
- 2016
-
Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 113, s. 5922-5927
-
Tidskriftsartikel (refereegranskat)abstract
- Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze oxidative cleavage of glycosidic bonds using molecular oxygen and an external electron donor. We have used NMR and isothermal titration calorimetry (ITC) to study the interactions of a broad-specificity fungal LPMO, NcLPMO9C, with various substrates and with cellobiose dehydrogenase (CDH), a known natural supplier of electrons. The NMR studies revealed interactions with cellohexaose that center around the copper site. NMR studies with xyloglucans, i. e., branched beta-glucans, showed an extended binding surface compared with cellohexaose, whereas ITC experiments showed slightly higher affinity and a different thermodynamic signature of binding. The ITC data also showed that although the copper ion alone hardly contributes to affinity, substrate binding is enhanced for metal-loaded enzymes that are supplied with cyanide, a mimic of O-2(-). Studies with CDH and its isolated heme b cytochrome domain unambiguously showed that the cytochrome domain of CDH interacts with the copper site of the LPMO and that substrate binding precludes interaction with CDH. Apart from providing insights into enzyme-substrate interactions in LPMOs, the present observations shed new light on possible mechanisms for electron supply during LPMO action.
|
|
| 8. |
- Knecht, Wolfgang, et al.
(författare)
-
Drosophila melanogaster deoxyribonucleoside kinase activates gemcitabine
- 2009
-
Ingår i: Biochemical and Biophysical Research Communications. - : Elsevier BV. - 1090-2104 .- 0006-291X. ; 382:2, s. 430-433
-
Tidskriftsartikel (refereegranskat)abstract
- Drosophila melanogaster multisubstrate deoxyribonucleoside kinase (Dm-dNK) can additionally sensitize human cancer cell lines towards the anti-cancer drug gemcitabine. We show that this property is based on the Dm-dNK ability to efficiently phosphorylate gemcitabine. The 2.2 angstrom resolution structure of DmdNK in complex with gemcitabine shows that the residues Tyr70 and Arg105 play a crucial role in the firm positioning of gemcitabine by extra interactions made by the fluoride atoms. This explains why gemcitabine is a good substrate for Dm-dNK(. (C) 2009 Elsevier Inc. All rights reserved.
|
|
| 9. |
- Borisova, Anna, et al.
(författare)
-
Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity
- 2015
-
Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 290, s. 22955-22969
-
Tidskriftsartikel (refereegranskat)abstract
- The recently discovered lytic polysaccharide monooxygenases (LPMOs) carry out oxidative cleavage of polysaccharides and are of major importance for efficient processing of biomass. NcLPMO9C from Neurospora crassa acts both on cellulose and on non-cellulose beta-glucans, including cellodextrins and xyloglucan. The crystal structure of the catalytic domain of NcLPMO9C revealed an extended, highly polar substrate-binding surface well suited to interact with a variety of sugar substrates. The ability of NcLPMO9C to act on soluble substrates was exploited to study enzyme-substrate interactions. EPR studies demonstrated that the Cu2+-center environment is altered upon substrate binding, whereas isothermal titration calorimetry studies revealed binding affinities in the low micromolar range for polymeric substrates that are due in part to the presence of a carbohydrate-binding module (CBM1). Importantly, the novel structure of NcLPMO9Cenabled a comparative study, revealing that the oxidative regioselectivity of LPMO9s (C1, C4, or both) correlates with distinct structural features of the copper coordination sphere. In strictly C1-oxidizing LPMO9s, access to the solvent-facing axial coordination position is restricted by a conserved tyrosine residue, whereas access to this same position seems unrestricted in C4-oxidizing LPMO9s. LPMO9s known to produce a mixture of C1- and C4- oxidized products show an intermediate situation.
|
|
| 10. |
- Borisova, Anna, et al.
(författare)
-
The method of integrated kinetics and its applicability to the exo-glycosidase-catalyzed hydrolyses of p-nitrophenyl glycosides.
- 2015
-
Ingår i: Carbohydrate Research. - : Elsevier BV. - 1873-426X .- 0008-6215. ; 412, s. 43-49
-
Tidskriftsartikel (refereegranskat)abstract
- In the present work we suggest an efficient method, using the whole time course of the reaction, whereby parameters kcat, Km and product KI for the hydrolysis of a p-nitrophenyl glycoside by an exo-acting glycoside hydrolase can be estimated in a single experiment. Its applicability was demonstrated for three retaining exo-glycoside hydrolases, β-xylosidase from Aspergillus awamori, β-galactosidase from Penicillium sp. and α-galactosidase from Thermotoga maritima (TmGalA). During the analysis of the reaction course catalyzed by the TmGalA enzyme we had observed that a non-enzymatic process, mutarotation of the liberated α-d-galactose, affected the reaction significantly.
|
|
